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Gene: TMEM5 |
Gene summary for TMEM5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMEM5 | Gene ID | 10329 |
| Gene name | ribitol xylosyltransferase 1 | |
| Gene Alias | HP10481 | |
| Cytomap | 12q14.2 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | G3V1K2 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 10329 | TMEM5 | P76T-E | Human | Esophagus | ESCC | 9.07e-17 | 3.91e-01 | 0.1207 |
| 10329 | TMEM5 | P79T-E | Human | Esophagus | ESCC | 5.11e-21 | 3.90e-01 | 0.1154 |
| 10329 | TMEM5 | P80T-E | Human | Esophagus | ESCC | 1.27e-29 | 9.34e-01 | 0.155 |
| 10329 | TMEM5 | P82T-E | Human | Esophagus | ESCC | 1.25e-05 | 3.77e-01 | 0.1072 |
| 10329 | TMEM5 | P83T-E | Human | Esophagus | ESCC | 6.01e-26 | 6.61e-01 | 0.1738 |
| 10329 | TMEM5 | P84T-E | Human | Esophagus | ESCC | 1.65e-03 | 2.72e-01 | 0.0933 |
| 10329 | TMEM5 | P89T-E | Human | Esophagus | ESCC | 1.86e-13 | 7.98e-01 | 0.1752 |
| 10329 | TMEM5 | P91T-E | Human | Esophagus | ESCC | 4.28e-15 | 1.11e+00 | 0.1828 |
| 10329 | TMEM5 | P107T-E | Human | Esophagus | ESCC | 9.65e-26 | 6.40e-01 | 0.171 |
| 10329 | TMEM5 | P127T-E | Human | Esophagus | ESCC | 1.58e-15 | 2.28e-01 | 0.0826 |
| 10329 | TMEM5 | P128T-E | Human | Esophagus | ESCC | 2.20e-45 | 1.25e+00 | 0.1241 |
| 10329 | TMEM5 | P130T-E | Human | Esophagus | ESCC | 3.25e-40 | 6.23e-01 | 0.1676 |
| 10329 | TMEM5 | C04 | Human | Oral cavity | OSCC | 8.85e-17 | 7.32e-01 | 0.2633 |
| 10329 | TMEM5 | C21 | Human | Oral cavity | OSCC | 1.06e-36 | 1.15e+00 | 0.2678 |
| 10329 | TMEM5 | C30 | Human | Oral cavity | OSCC | 9.78e-34 | 1.49e+00 | 0.3055 |
| 10329 | TMEM5 | C38 | Human | Oral cavity | OSCC | 7.06e-05 | 7.62e-01 | 0.172 |
| 10329 | TMEM5 | C43 | Human | Oral cavity | OSCC | 2.48e-25 | 4.96e-01 | 0.1704 |
| 10329 | TMEM5 | C46 | Human | Oral cavity | OSCC | 3.28e-17 | 4.76e-01 | 0.1673 |
| 10329 | TMEM5 | C51 | Human | Oral cavity | OSCC | 2.85e-11 | 6.48e-01 | 0.2674 |
| 10329 | TMEM5 | C57 | Human | Oral cavity | OSCC | 4.03e-03 | 2.82e-01 | 0.1679 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00458619 | Breast | Precancer | negative regulation of proteolysis | 50/1080 | 351/18723 | 2.99e-09 | 2.39e-07 | 50 |
| GO:00098969 | Breast | Precancer | positive regulation of catabolic process | 48/1080 | 492/18723 | 2.62e-04 | 3.84e-03 | 48 |
| GO:00313319 | Breast | Precancer | positive regulation of cellular catabolic process | 43/1080 | 427/18723 | 2.75e-04 | 4.00e-03 | 43 |
| GO:19043757 | Breast | Precancer | regulation of protein localization to cell periphery | 15/1080 | 125/18723 | 5.58e-03 | 4.07e-02 | 15 |
| GO:19054757 | Breast | Precancer | regulation of protein localization to membrane | 19/1080 | 175/18723 | 5.98e-03 | 4.22e-02 | 19 |
| GO:00516047 | Breast | Precancer | protein maturation | 28/1080 | 294/18723 | 6.45e-03 | 4.50e-02 | 28 |
| GO:19030767 | Breast | Precancer | regulation of protein localization to plasma membrane | 13/1080 | 104/18723 | 6.79e-03 | 4.65e-02 | 13 |
| GO:004586114 | Breast | IDC | negative regulation of proteolysis | 70/1434 | 351/18723 | 8.21e-14 | 2.22e-11 | 70 |
| GO:000989614 | Breast | IDC | positive regulation of catabolic process | 62/1434 | 492/18723 | 7.06e-05 | 1.42e-03 | 62 |
| GO:190547513 | Breast | IDC | regulation of protein localization to membrane | 28/1434 | 175/18723 | 1.56e-04 | 2.71e-03 | 28 |
| GO:003133114 | Breast | IDC | positive regulation of cellular catabolic process | 54/1434 | 427/18723 | 1.85e-04 | 3.07e-03 | 54 |
| GO:190307613 | Breast | IDC | regulation of protein localization to plasma membrane | 17/1434 | 104/18723 | 2.28e-03 | 2.09e-02 | 17 |
| GO:190437513 | Breast | IDC | regulation of protein localization to cell periphery | 19/1434 | 125/18723 | 3.06e-03 | 2.60e-02 | 19 |
| GO:005160413 | Breast | IDC | protein maturation | 35/1434 | 294/18723 | 6.18e-03 | 4.40e-02 | 35 |
| GO:00726599 | Breast | IDC | protein localization to plasma membrane | 34/1434 | 284/18723 | 6.33e-03 | 4.47e-02 | 34 |
| GO:004586123 | Breast | DCIS | negative regulation of proteolysis | 63/1390 | 351/18723 | 4.39e-11 | 6.06e-09 | 63 |
| GO:000989624 | Breast | DCIS | positive regulation of catabolic process | 61/1390 | 492/18723 | 5.32e-05 | 1.09e-03 | 61 |
| GO:003133124 | Breast | DCIS | positive regulation of cellular catabolic process | 54/1390 | 427/18723 | 8.34e-05 | 1.58e-03 | 54 |
| GO:190547522 | Breast | DCIS | regulation of protein localization to membrane | 26/1390 | 175/18723 | 5.31e-04 | 6.88e-03 | 26 |
| GO:190307623 | Breast | DCIS | regulation of protein localization to plasma membrane | 16/1390 | 104/18723 | 4.13e-03 | 3.27e-02 | 16 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| TMEM5 | SNV | Missense_Mutation | novel | c.1220N>C | p.Lys407Thr | p.K407T | Q9Y2B1 | protein_coding | deleterious(0.01) | probably_damaging(0.961) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TMEM5 | SNV | Missense_Mutation | c.287N>T | p.Thr96Ile | p.T96I | Q9Y2B1 | protein_coding | tolerated(0.11) | benign(0.003) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| TMEM5 | SNV | Missense_Mutation | novel | c.739G>A | p.Ala247Thr | p.A247T | Q9Y2B1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-OL-A6VQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TMEM5 | SNV | Missense_Mutation | novel | c.239G>A | p.Arg80Lys | p.R80K | Q9Y2B1 | protein_coding | tolerated(0.38) | benign(0.009) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| TMEM5 | SNV | Missense_Mutation | rs570064856 | c.154G>C | p.Glu52Gln | p.E52Q | Q9Y2B1 | protein_coding | tolerated(0.39) | benign(0.221) | TCGA-VS-A9UU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TMEM5 | SNV | Missense_Mutation | c.559N>G | p.Leu187Val | p.L187V | Q9Y2B1 | protein_coding | deleterious(0) | possibly_damaging(0.861) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| TMEM5 | SNV | Missense_Mutation | c.559N>G | p.Leu187Val | p.L187V | Q9Y2B1 | protein_coding | deleterious(0) | possibly_damaging(0.861) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR | |
| TMEM5 | SNV | Missense_Mutation | novel | c.724N>C | p.Trp242Arg | p.W242R | Q9Y2B1 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TMEM5 | SNV | Missense_Mutation | novel | c.1133N>T | p.Ser378Phe | p.S378F | Q9Y2B1 | protein_coding | deleterious(0.02) | possibly_damaging(0.568) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TMEM5 | SNV | Missense_Mutation | novel | c.316G>A | p.Ala106Thr | p.A106T | Q9Y2B1 | protein_coding | deleterious(0.03) | probably_damaging(0.998) | TCGA-AJ-A2QO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
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